Updating workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 from 0.3 to 0.4

Author: planemo-autoupdate

workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga

@@ -11,7 +11,7 @@
     ],
     "format-version": "0.1",
     "license": "BSD-3-Clause",
-    "release": "0.3",
+    "release": "0.4",
     "name": "Assembly-decontamination-VGP9",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n### Worflow ran on: \n\n```galaxy\ninvocation_time()\n```\n\n# List of contaminants\n\n\r\n```galaxy\nhistory_dataset_as_table(output=\"contaminants_table\")\n```\r\n\n\n# List of Mitochondrial scaffolds\n\r\n```galaxy\nhistory_dataset_as_table(output=\"mito_scaff_names\")\n```\r\n\n\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
@@ -64,7 +64,7 @@
                 "top": 692.7734375
             },
             "tool_id": null,
-            "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
+            "tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
             "tool_version": null,
             "type": "parameter_input",
             "uuid": "4bd1b150-bdb0-4458-9ddc-62bc29356aa2",
@@ -88,7 +88,12 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool NCBI BLAST+ dustmasker",
+                    "name": "db_opts"
+                }
+            ],
             "label": "soft-masking ",
             "name": "NCBI BLAST+ dustmasker",
             "outputs": [
@@ -124,7 +129,7 @@
         },
         "3": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy0",
             "errors": null,
             "id": 3,
             "input_connections": {
@@ -160,15 +165,15 @@
                     "output_name": "output"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "86755160afbf",
+                "changeset_revision": "3dc70b59608c",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"/^>/!y/atcgn/NNNNN/\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "9.3+galaxy1",
+            "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"/^>/!y/atcgn/NNNNN/\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "9.5+galaxy0",
             "type": "tool",
             "uuid": "5089350b-c1a9-498a-9786-9864d484f77a",
             "when": null,
@@ -189,7 +194,12 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Kraken2",
+                    "name": "single_paired"
+                }
+            ],
             "label": "ID non-target contaminants",
             "name": "Kraken2",
             "outputs": [
@@ -448,7 +458,7 @@
                 }
             },
             "tool_id": "Cut1",
-            "tool_state": "{\"columnList\": \"c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"columnList\": \"c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "1.0.2",
             "type": "tool",
             "uuid": "8cc3e58f-2940-454a-9cf6-b32c1ab19016",
@@ -457,7 +467,7 @@
         },
         "10": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy0",
             "errors": null,
             "id": 10,
             "input_connections": {
@@ -486,15 +496,15 @@
                 "top": 423.9453125
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "86755160afbf",
+                "changeset_revision": "3dc70b59608c",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "9.3+galaxy1",
+            "tool_version": "9.5+galaxy0",
             "type": "tool",
             "uuid": "5b7e33a0-0ec4-4539-bb91-0c862597df69",
             "when": null,
@@ -508,7 +518,7 @@
         },
         "11": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy3",
             "errors": null,
             "id": 11,
             "input_connections": {
@@ -521,7 +531,20 @@
                     "output_name": "out_file1"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool gfastats",
+                    "name": "mode_condition"
+                },
+                {
+                    "description": "runtime parameter for tool gfastats",
+                    "name": "target_condition"
+                },
+                {
+                    "description": "runtime parameter for tool gfastats",
+                    "name": "target_condition"
+                }
+            ],
             "label": "removing scaffolds ",
             "name": "gfastats",
             "outputs": [
@@ -535,15 +558,15 @@
                 "top": 798.078125
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy3",
             "tool_shed_repository": {
-                "changeset_revision": "3ef480892a9f",
+                "changeset_revision": "0393c0415171",
                 "name": "gfastats",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta.gz\", \"__current_case__\": 1, \"line_length\": null}, \"discover_paths\": false, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"true\", \"__current_case__\": 1, \"target_sequence\": \"\", \"include_bed\": {\"__class__\": \"ConnectedValue\"}, \"exclude_bed\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.3.6+galaxy0",
+            "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta.gz\", \"__current_case__\": 1, \"line_length\": null}, \"discover_paths\": false, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"true\", \"__current_case__\": 1, \"target_sequence\": \"\", \"include_bed\": {\"__class__\": \"ConnectedValue\"}, \"exclude_bed\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.3.9+galaxy3",
             "type": "tool",
             "uuid": "5113c945-c811-4cbc-81ac-20d1d80e97ed",
             "when": null,

workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## [0.4] 2025-03-10
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy3`
+
 ## [0.3] - 2024-08-26
 
 - Changed the regex to only change the sequences. The workflow is now more robust to different (non VGP) scaffold names and VGP names with prefixes.